Problems restoring files with Time Machine after hard drive failure

Hello everyone,
I had a Mavericks (10.9.5) installation on my Mac Mini when my hard drive suddenly "died". I therefore replaced the hard drive with a new one and started the recovery mode using the cmd + R keyboard shortcut during booting. I then partitioned and formated the new hard drive and afterwards selectd "Restore from Time Machine Backup" (see the screenshot on the following page: https://www.apple.com/osx/recovery/). To my surprise, the following error message was displayed: "An error occurred while adding a recovery system to the destination disk". After some research, I discovered that this problem is probably caused by a Mountain Lion installation bug (http://macdailynews.com/2013/02/28/new-macs-suffering-from-os-x-mountain-lion-in stallation-bug/). This leads to my first question:
1) Why does the recovery mode start the Mountain Lion (10.8.5) installer and not the Mavericks (10.9.5) installer?
Anyway, since this problem left me no alternative, I selected "Reinstall OS X" instead, which downloaded Mountain Lion from the Internet. After the installation was complete, I used Migration Assistant to recover my two accounts, their apps and data. However, after the process was completed, I discovered that some files were missing in a folder that I was using before the hard drive "died". This leads to my second question:
2) Why are some files missing from that folder?
Anyway, I though I could quickly recover these lost files by entering Time Machine. I did that and selected the respective folder. However, having that folder or any other folder selected, Time Machine doesn't display any previous back-ups on its timeline although the latter goes back as far as 26 August 2013.
3) Why doesn't Time Machine display older versions of that folder on its timeline?
I will greatly appreciate any help!

Try E2/4 in the 1st linked article.
Time Machine Troubleshooting
Time Machine Troubleshooting Problems
James Pond (Pondini) died last year unfortunately.

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Sadly it didn't help me either.
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